It may be that you are on a version of puppet where there are issues with location information. The latest puppet produces file and line information for that warning.

The error occurs on the master side. In the latest version the warning is only issued if master --debug is on, the message is otherwise ignored. The cause is something like File[undef] (or some other resource type than File), or Class[undef]. Most likely caused by an expression that results in empty string or undef.

Try a puppet apply and see if that gives you file/line. If it does please file an issue for Puppet Server about location information missing.

Comments

I am currently running puppet server 1.2.0 / puppet 3.8.7 ( migration process to puppet 4.x is ongoing tough, so it's a good thing that the latest version provides more infos )
puppet apply doesn't give more clues, but I will have a look at the possible resources undef expressions